##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CellBarcode.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CellBarcode_1.13.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/CellBarcode.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘CellBarcode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellBarcode’ version ‘1.13.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CellBarcode’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      3.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bc_extract_sc_fastq: no visible binding for global variable
  ‘cell_barcode’
bc_extract_sc_fastq: no visible binding for global variable ‘umi’
bc_extract_sc_fastq: no visible binding for global variable
  ‘barcode_seq’
process_sc_list: no visible binding for global variable ‘cell_barcode’
process_sc_list: no visible binding for global variable ‘umi’
process_sc_list: no visible binding for global variable ‘barcode_seq’
bc_2matrix,BarcodeObj: no visible binding for global variable
  ‘barcode_seq’
bc_cure_depth,BarcodeObj : <anonymous>: no visible binding for global
  variable ‘barcode_seq’
bc_cure_umi,BarcodeObj : <anonymous>: no visible binding for global
  variable ‘barcode_seq’
bc_cure_umi,BarcodeObj : <anonymous>: no visible binding for global
  variable ‘umi_seq’
bc_extract,data.frame: no visible binding for global variable ‘umi_seq’
bc_extract,data.frame: no visible binding for global variable
  ‘barcode_seq’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘barcode_read_count’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘raw_read_count’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘umi_seq’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘barcode_seq’
bc_plot_count,BarcodeObj: no visible binding for global variable
  ‘cell_barcode’
bc_plot_count,BarcodeObj: no visible binding for global variable ‘V1’
bc_plot_count,BarcodeObj: no visible binding for global variable ‘x’
bc_plot_seqQc,BarcodeQcSet: no visible binding for global variable
  ‘sample_name’
bc_subset,BarcodeObj : <anonymous>: no visible binding for global
  variable ‘barcode_seq’
Undefined global functions or variables:
  V1 barcode_read_count barcode_seq cell_barcode raw_read_count
  sample_name umi umi_seq x
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.21-bioc/R/site-library/CellBarcode/libs/CellBarcode.so’:
  Found ‘abort’, possibly from ‘abort’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/CellBarcode.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CellBarcode
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CellBarcode’ ...
** this is package ‘CellBarcode’ version ‘1.13.2’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
rm -Rf CellBarcode.so ./rust/target/release/libCellBarcode.a entrypoint.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -c entrypoint.c -o entrypoint.o
# In some environments, ~/.cargo/bin might not be included in PATH, so we need
# to set it here to ensure cargo can be invoked. It is appended to PATH and
# therefore is only used if cargo is absent from the user's PATH.
if [ "" != "true" ]; then \
	export CARGO_HOME=/home/biocbuild/bbs-3.21-bioc/meat/CellBarcode/src/.cargo; \
fi && \
	export PATH="/home/biocbuild/.virtualenvs/r-reticulate/bin:/usr/local/bin:/usr/bin:/bin:/snap/bin:/home/biocbuild/.dotnet/tools:/home/biocbuild/.cargo/bin" && \
	cargo build --lib --release --manifest-path=./rust/Cargo.toml --target-dir ./rust/target
    Updating crates.io index
 Downloading crates ...
  Downloaded adler2 v2.0.0
  Downloaded leven-distance v1.0.0
  Downloaded cfg-if v1.0.0
  Downloaded paste v1.0.15
  Downloaded either v1.14.0
  Downloaded quote v1.0.38
  Downloaded extendr-macros v0.7.1
  Downloaded unicode-ident v1.0.17
  Downloaded proc-macro2 v1.0.93
  Downloaded memchr v2.7.4
  Downloaded itertools v0.10.5
  Downloaded flate2 v1.1.0
  Downloaded extendr-api v0.7.1
  Downloaded aho-corasick v1.1.3
  Downloaded once_cell v1.20.3
  Downloaded regex v1.11.1
  Downloaded miniz_oxide v0.8.5
  Downloaded syn v2.0.98
  Downloaded regex-syntax v0.8.5
  Downloaded crc32fast v1.4.2
  Downloaded lazy_static v1.5.0
  Downloaded regex-automata v0.4.9
  Downloaded libR-sys v0.7.1
   Compiling proc-macro2 v1.0.93
   Compiling unicode-ident v1.0.17
   Compiling libR-sys v0.7.1
   Compiling memchr v2.7.4
   Compiling paste v1.0.15
   Compiling adler2 v2.0.0
   Compiling regex-syntax v0.8.5
   Compiling cfg-if v1.0.0
   Compiling extendr-api v0.7.1
   Compiling either v1.14.0
   Compiling once_cell v1.20.3
   Compiling lazy_static v1.5.0
   Compiling leven-distance v1.0.0
   Compiling crc32fast v1.4.2
   Compiling miniz_oxide v0.8.5
   Compiling itertools v0.10.5
   Compiling aho-corasick v1.1.3
   Compiling flate2 v1.1.0
   Compiling quote v1.0.38
   Compiling syn v2.0.98
   Compiling regex-automata v0.4.9
   Compiling regex v1.11.1
   Compiling extendr-macros v0.7.1
   Compiling CellBarcode v0.1.0 (/home/biocbuild/bbs-3.21-bioc/meat/CellBarcode/src/rust)
warning: crate `CellBarcode` should have a snake case name
  |
  = help: convert the identifier to snake case: `cell_barcode`
  = note: `#[warn(non_snake_case)]` on by default

warning: `CellBarcode` (lib) generated 1 warning
    Finished release [optimized] target(s) in 55.57s
if [ "" != "true" ]; then \
	rm -Rf /home/biocbuild/bbs-3.21-bioc/meat/CellBarcode/src/.cargo && \
	rm -Rf ./rust/target/release/build; \
fi
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o CellBarcode.so entrypoint.o -L./rust/target/release -lCellBarcode -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-CellBarcode/00new/CellBarcode/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CellBarcode)

R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CellBarcode)
> 
> test_check("CellBarcode")
------------
bc_cure_depth: isUpdate is FALSE, use messyBc as input.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is FALSE, use messyBc as input.
------------
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: BiocParallel
Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: Rsamtools
Loading required package: GenomicRanges
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
------------
bc_cure_depth: isUpdate is TRUE, update the cleanBc.
------------
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 38 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• On CRAN (3): 'test-BarcodeObj.R:119:3', 'test-describ.R:51:3',
  'test-qc.R:17:3'

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 38 ]
> 
> proc.time()
   user  system elapsed 
 11.775   0.628  12.233